Proposed priority for the first release

ruiwanguk commented 9 years ago

@jadianes @jgriss @noedelta Since our last dev release, we had a lot of releases and discussions for the potential improvements. After discussing with Jose and Johannes, here are a proposed list of todos for the first production release (they are ordered by priority)

For the peptide search result page:

[x] Show modifications for the peptide sequences
[x] Faceting peptide search results for both species and modifications
[x] Improve the relevance score for the search results (#spectra first, then max ratio)
[x] Hide bubble chart

For the cluster summary page:

[x] Show modifications together with peptide sequence
[x] Fix the problem with the strange character with paging the original projects
[x] Fix the problem with the modification pie chart at both the web service level and the front end level
[x] Improve the paging of the unique peptide section, hide the pagination when results can be fitted on one page
[x] Remove the number of modifications from the summary section
[x] Sort by the number of PSMs for the table of unique peptides
[x] Show modifications on the peptides at the table of unique peptides
[x] Add number of projects for unique peptides

For the home page:

[x] Provide real cluster statistics
[x] Provide detailed descriptions for each sections
[x] Provide newly structured home page as the mockup suggests
[x] Provide documentations on the help page and the about page
[x] Add citation as part of PRIDE Cluster summary

For spectrum library page:

[x] Update introduction
[x] Update the code snippets
[x] Move the release date and version next to the title “Latest Release” with smaller font
[x] Change “Using the PRIDE Spectrum Libraries” to “How to use spectrum libraries"
[x] Increase the gap between “Latest release” and “ Using the PRID Spectrum libraries"

ToDo for the future:

[ ] Add sorting to the peptide search page
[ ] Provide bubble chart as suggested by the mockup for the peptide search page
[x] Improve performance of loading original projects for the cluster summary page
[ ] Add downloading of consensus spectrum as MGF
[ ] Click the unique peptides to view PSM details

Let me know if I have missed anything, I would suggest that we tick off these todos once they are done.

jadianes commented 9 years ago

I've added:

[x] Show modifications together with peptide sequence to the Cluster summary page (that I use to call Cluster details page by the way :) )

ruiwanguk commented 9 years ago

I have fixed the web service side of the problem on providing modifications and species distribution. Will deploy this in the afternoon.

ruiwanguk commented 9 years ago

I have added the number of projects to the unique peptide WS end point, so that we can display the number of projects for each unique peptide.

ruiwanguk commented 9 years ago

Improve the performance of retrieving project details using multi threaded approach. This is still limited by the speed of PRIDE Archive web service, which can be slow at times.

[X] Improve performance of loading original projects for the cluster summary page

ruiwanguk commented 9 years ago

The general statistics are now provided

[x] Provide real cluster statistics

jadianes commented 9 years ago

Done

[x] Hide bubble chart

jadianes commented 9 years ago

Done

[x] Improve the paging of the unique peptide section, hide the pagination when results can be fitted on one page
[x] Remove the number of modifications from the summary section
[x] Show modifications on the peptides at the table of unique peptides
[x] Add number of projects for unique peptides

PRIDE-Cluster / cluster-web-app

Proposed priority for the first release #37